Chord Plot

Authors

[Editor] Hu Zheng;

[Contributors]

Note

Hiplot website

This page is the tutorial for source code version of the Hiplot Chord Plot plugin. You can also use the Hiplot website to achieve no code ploting. For more information please see the following link:

https://hiplot.cn/basic/chord?lang=en

The complex interaction is visualized in the form of chord graph.

Setup

System Requirements: Cross-platform (Linux/MacOS/Windows)
Programming language: R
Dependent packages: circlize; ggplotify

# Install packages
if (!requireNamespace("circlize", quietly = TRUE)) {
  install.packages("circlize")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}

# Load packages
library(circlize)
library(ggplotify)

Data Preparation

Data frame or matrix of interaction of genes with pathways or gene ontologys.

# Load data
data <- read.table("files/Hiplot/020-chord-data.txt", header = T)

# convert data structure
row.names(data) <- data[, 1]
data <- data[, -1]
data <- as.matrix(data)

# View data
head(data)

   E1 E2 E3 E4 E5
S1  4 16 12 18 11
S2  7 11  2 15 10
S3  9  2 17 16 11
S4 14  9 12  3 17
S5  1  1  7  1 12
S6 10 18  9 13  9

Visualization

# Chord Plot
Palette <- c("#E64B35FF","#4DBBD5FF","#00A087FF","#3C5488FF","#F39B7FFF",
             "#8491B4FF","#91D1C2FF","#DC0000FF","#7E6148FF","#B09C85FF")
grid.col <- c(Palette, Palette, Palette[1:5])
p <- as.ggplot(function() {
  chordDiagram(
    data, grid.col = grid.col, grid.border = NULL, transparency = 0.5,
    row.col = NULL, column.col = NULL,  order = NULL,
    directional = 0, # 1, -1, 0, 2
    direction.type = "diffHeight", # diffHeight and arrows
    diffHeight = convert_height(2, "mm"), reduce = 1e-5, xmax = NULL, 
    self.link = 2, symmetric = FALSE, keep.diagonal = FALSE, 
    preAllocateTracks = NULL,
    annotationTrack = c("name", "grid", "axis"),
    annotationTrackHeight = convert_height(c(3, 3), "mm"),
    link.border = NA, link.lwd = par("lwd"), link.lty = par("lty"), 
    link.sort = FALSE, link.decreasing = TRUE, link.largest.ontop = FALSE,
    link.visible = T, link.rank = NULL, link.overlap = FALSE,
    scale = F, group = NULL, big.gap = 10, small.gap = 1
    )
  })

p